Targeting Non-B-Form DNA in Living Cells

Du, Yuhao; Zhou, Xiang

doi:10.1002/tcr.201300005

Cited by 42 publications

(31 citation statements)

References 122 publications

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“…normal vs. cancer cells). Moreover, considering the renewed interest in therapeutic targeting of DNA/RNA with small molecular weight compounds , it is plausible that the in vivo profiling of NA drug candidates will become one of the most important applications of in‐cell NMR in the future.…”

Section: Discussionmentioning

confidence: 99%

“…Nucleic acids (NAs) are abundant biopolymers found in all living entities, where NAs encode, transmit and express genetic information. Due to their biological roles, NAs represent inherently important targets for drug development . In addition, the unique nanoscale geometry, biocompatibility, biodegradability and molecular recognition capacity of NAs has made NAs promising candidates for the construction of novel functional nanomaterials and biosensors for a broad range of in vivo applications .…”

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confidence: 99%

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Advances in the cellular structural biology of nucleic acids

et al. 2018

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Conventional biophysical and chemical biology approaches for delineating relationships between the structure and biological function of nucleic acids (NAs) abstract NAs from their native biological context. However, cumulative experimental observations have revealed that the structure, dynamics and interactions of NAs might be strongly influenced by a broad spectrum of specific and nonspecific physical-chemical environmental factors. This consideration has recently sparked interest in the development of novel tools for structural characterization of NAs in the native cellular context. Here, we review the individual methods currently being employed for structural characterization of NA structure in a native cellular environment with a focus on recent advances and developments in the emerging fields of in-cell NMR and electron paramagnetic resonance spectroscopy and in-cell single-molecule FRET of NAs.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Advances in the cellular structural biology of nucleic acids

et al. 2018

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“…In these two constructs the individual U and P elements were cloned in different spatial arrangements. Fis and H-NS were purified as previously described (69,70).…”

Section: Constructsmentioning

confidence: 99%

DNA sequence-directed cooperation between nucleoid-associated proteins

Japaridze

Yang

Dekker

et al. 2020

Preprint

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Nucleoid associated proteins (NAPs) are a class of highly abundant DNA binding proteins in bacteria and archaea. While the composition and relative abundance of the NAPs change during the bacterial growth cycle, surprisingly little is known about their crosstalk in mutually binding to the bacterial chromosome and stabilising higher-order nucleoprotein complexes. Here, we use atomic force microscopy and solid-state nanopores to investigate longrange nucleoprotein structures formed by the binding of two major NAPs, FIS and H-NS, to DNA molecules with distinct binding-site arrangements. We find that spatial organisation of the protein binding sites can govern the higher-order architecture of the nucleoprotein complexes. Based on sequence arrangement the complexes differed in their global shape and compaction, as well as the extent of FIS and H-NS binding. Our observations highlight the important role the DNA sequence plays in driving structural differentiations within the bacterial chromosome.

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“…Among these building molecules, nucleic acids attract particular attention owing to their easy synthesis, simple operation, sequence‐specific recognition property, and a robust physicochemical nature. Especially, nucleic acids are polymorphic macromolecules and exist in a variety of secondary structures, including duplex, triplex, G‐quadruplex, i‐motif, bulge, hairpin, three‐way and four‐way junction, left‐handed Z‐form, and A‐form, depending on their sequences and different environment conditions . Besides classical Watson‐Crick base pairing interactions, non‐covalent bonds through π‐π stacking, hydrogen bonds, hydrophobic interactions, and van der Waals interactions also involve in the formation of these secondary structures.…”

Section: Introductionmentioning

confidence: 99%

Nucleic Acids and Smart Materials: Advanced Building Blocks for Logic Systems

Ren

2014

Advanced Materials

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Logic gates can convert input signals into a defined output signal, which is the fundamental basis of computing. Inspired by molecular switching from one state to another under an external stimulus, molecular logic gates are explored extensively and recognized as an alternative to traditional silicon-based computing. Among various building blocks of molecular logic gates, nucleic acid attracts special attention owing to its specific recognition abilities and structural features. Functional materials with unique physical and chemical properties offer significant advantages and are used in many fields. The integration of nucleic acids and functional materials is expected to bring about several new phenomena. In this Progress Report, recent progress in the construction of logic gates by combining the properties of a range of smart materials with nucleic acids is introduced. According to the structural characteristics and composition, functional materials are categorized into three classes: polymers, noble-metal nanomaterials, and inorganic nanomaterials. Furthermore, the unsolved problems and future challenges in the construction of logic gates are discussed. It is hoped that broader interests in introducing new smart materials into the field are inspired and tangible applications for these constructs are found.

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Targeting Non-B-Form DNA in Living Cells

Cited by 42 publications

References 122 publications

Advances in the cellular structural biology of nucleic acids

Advances in the cellular structural biology of nucleic acids

DNA sequence-directed cooperation between nucleoid-associated proteins

Nucleic Acids and Smart Materials: Advanced Building Blocks for Logic Systems

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